Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

Help for "Molecule as Layers" webapplication [Go to application]

  1. Molecule as layers is a webapplication that implements Layers algorithm.
  2. You can submit coordinate file in PDB format or a ZIP of pdb files for Layer to work.
  3. Please do NOT include any subfolders in the zip file.
  4. After successful completion of processing, an email will be sent to the provided e-mail ID, with all the peeled layers with extensions as follows:
  5. If xxx.pdb file is submitted and if default Sr is chosen, and if Layers extract 3 layers from the molecule, then the output files will be xxx.surf1, xxx.surf2, xxx.surf3.
  6. Where xxx.surf1 contains atoms of surface layer, xxx.surf2 is the layer beneath the surface layer and finally xxx.surf3 is the innermost layer of the structure.
  7. If any structure is peeled to more than 3 layers then the xxx.surf1 is the surface layer, xxx.surf2 followed by xxx.surf3 and so on are sandwich layers, and[N] where N is the highest number for layer of that macromolecular structure is the innermost layer.
  8. xxx.RTP is the file containing sorted details of residues and their respective layer number.
  9. If Sr changes from default, then the naming convention changes. Output file names will appear as xxx_Sr.sampl Where Sr is the provided value by user.
  10. Note:

  11. You are NOT asked to submit the chain ID, so please submit the PDB file containing the chains that you want Layers to peel.
  12. If a macromolecular complex file is submitted, then the surface of the complex is extracted.

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